[PyMOL] view's in pymol and movie

Hello again pymolers I have a question about the view matrices. Basically I would like to go from one view to another view gradually in a movie. Is there a way to calculate from the view matrices, how much I need to rotate around x,y, and Z and move in x, y and z? I'm sure it can be done, but h

[PyMOL] pymol/apbs vs grasp

Has anyone noticed major differences between the results obtained in GRASP when using the method... 1) Read| PDB file 2) Read|Radius Charge File(+Assign) Input AMBER.crg 3) Build|Molecular Surface|All atoms 4) Calculate|New Potentail Map 5) Calculate|Pot. via Map at Surfaces/Atoms|All atoms

[PyMOL] density around ligand

Hi Jianhai, load yourmap.xplor isomesh map1, yourmap, 1.5, LIGAND, carve=1.6 color green, map1 show mesh, map1 The carve command allows you to selectively show density around whatever selection you want. I hope this gives you some ideas. You can also type "help isomesh" in the GUI to get a b

[PyMOL] re: pymol/apbs vs grasp

I have stumbled across the parameter causing the difference. In all of the examples distributed with APBS, the pdie (solute dielectric) value is set to 2.0 whereas ABPS-tools.py defaults this to 20.0. I find that if I use 2.0 instead of 20.0 for pdie, the resulting electrostatic potential map i

[PyMOL] view's in pymol and movie

Hi Mike, I use a nifty little script from Laurence Pearl/ Lieven Buts called camera_view_travel, which creates smooth transitions between multiple views of your molecule. I then call their script from my movie script. Here is my movie.pml and below that is camera_view_travel.py I hope thi

RE: [PyMOL] view's in pymol and movie

Mike, This may be the first public mention I've made of this, but recent betas include an experimental "mview" command than can be used to perform the same kind of interpolation as the scene transitions. Here is an example script: load $TUT/1hpv.pdb as ribbon show sticks, organic util.cbc elem c

Re: [PyMOL] re: pymol/apbs vs grasp

Hi Jack, > In all of the examples distributed with APBS, the pdie (solute dielectric) The pdie must be the protein dielectric constant though the comment for pdie in the pymol generated .in-file reads "# Solute dielectric" ... that is probably a mistake. The APBS-plugin says Protein Dielectric. T

Re: [PyMOL] re: pymol/apbs vs grasp

Richard, Actually I don't have a copy of Delphi available (hence the use of APBS). I did notice that I see more positive surface area on a molecule with a -13 net charge when the run is done with pdie of 2.0 compared to 20.0 even in the presence of 0.150 mM NaCl ions. I also noticed an oddity

[PyMOL] SEPs in pymol generated pqr

What is the recommended approach with apbs for creating a pqr file from a pdb which has SEP residues? Under gromacs I have been able to do MD on this peptide by using the user donated ffG43a1p force field which supports phosphoserine residues. Unfortunately none of the force fields available a

[PyMOL] view's in pymol and movie

Mike, The routines that Scott cites were nicely incorporated into MasterMovie.py by Seth Harris (shar...@msg.ucsf.edu) that is derived from Kristian Rother's rTools (www.rubor.de) and modified . Email Seth to see where he hides the program. Warren ... Glad to hear there is a new command i

[PyMOL] effect of mutation

Hi all, Yes, it worked for me, the problem is i was using the older version of pymol. Now the mutagenesis works. Now how to interprete the results of mutation and what are the different ways to see the effect of mutation in pymol thanks in avance regards sankari